MultifacetedProtDB - Bologna Biocomputing Group

Structure

PDB	Resolution (Å)	PDB name
2LY4		HMGB1-facilitated p53 DNA binding occurs via HMG-box/p53 transactivation domain interaction and is regulated by the acidic tail
2RTU		Solution structure of oxidized human HMGB1 A box
2YRQ		Solution structure of the tandem HMG box domain from Human High mobility group protein B1
6CG0	3.17	Cryo-EM structure of mouse RAG1/2 HFC complex (3.17 A)
6CIJ	3.9	Cryo-EM structure of mouse RAG1/2 HFC complex containing partial HMGB1 linker(3.9 A)
6CIK	3.15	Pre-Reaction Complex, RAG1(E962Q)/2-intact/nicked 12/23RSS complex in Mn2+
6CIL	4.15	PRE-REACTION COMPLEX, RAG1(E962Q)/2-INTACT/INTACT 12/23RSS COMPLEX IN MN2+
6CIM	3.6	Pre-Reaction Complex, RAG1(E962Q)/2-nicked/intact 12/23RSS complex in Mn2+
6OEM	3.6	Cryo-EM structure of mouse RAG1/2 PRC complex (DNA0)
6OEN	4.3	Cryo-EM structure of mouse RAG1/2 PRC complex (DNA1)
6OEO	3.69	Cryo-EM structure of mouse RAG1/2 NFC complex (DNA1)

GO term

GO ontology	GO term	GO description
Biological Process	GO:0032392	DNA geometric change
Biological Process	GO:0006310	DNA recombination
Biological Process	GO:0006265	DNA topological change
Biological Process	GO:0035711	T-helper 1 cell activation
Biological Process	GO:0045063	T-helper 1 cell differentiation
Biological Process	GO:0033151	V(D)J recombination
Biological Process	GO:0002218	activation of innate immune response
Biological Process	GO:0043277	apoptotic cell clearance
Biological Process	GO:0006914	autophagy
Biological Process	GO:0071222	cellular response to lipopolysaccharide
Biological Process	GO:0002407	dendritic cell chemotaxis
Biological Process	GO:0006303	double-strand break repair via nonhomologous end joining
Biological Process	GO:0031507	heterochromatin formation
Biological Process	GO:0006954	inflammatory response
Biological Process	GO:0002437	inflammatory response to antigenic stimulus
Biological Process	GO:0045087	innate immune response
Biological Process	GO:0001773	myeloid dendritic cell activation
Biological Process	GO:0043371	negative regulation of CD4-positive, alpha-beta T cell differentiation
Biological Process	GO:0017055	negative regulation of RNA polymerase II transcription preinitiation complex assembly
Biological Process	GO:2000426	negative regulation of apoptotic cell clearance
Biological Process	GO:0043537	negative regulation of blood vessel endothelial cell migration
Biological Process	GO:0000122	negative regulation of transcription by RNA polymerase II
Biological Process	GO:0032689	negative regulation of type II interferon production
Biological Process	GO:0031175	neuron projection development
Biological Process	GO:0097350	neutrophil clearance
Biological Process	GO:0043388	positive regulation of DNA binding
Biological Process	GO:0051106	positive regulation of DNA ligation
Biological Process	GO:0070374	positive regulation of ERK1 and ERK2 cascade
Biological Process	GO:0046330	positive regulation of JNK cascade
Biological Process	GO:0043410	positive regulation of MAPK cascade
Biological Process	GO:0042104	positive regulation of activated T cell proliferation
Biological Process	GO:0043065	positive regulation of apoptotic process
Biological Process	GO:0010508	positive regulation of autophagy
Biological Process	GO:0043536	positive regulation of blood vessel endothelial cell migration
Biological Process	GO:2000343	positive regulation of chemokine (C-X-C motif) ligand 2 production
Biological Process	GO:0043280	positive regulation of cysteine-type endopeptidase activity involved in apoptotic process
Biological Process	GO:0007204	positive regulation of cytosolic calcium ion concentration
Biological Process	GO:2001200	positive regulation of dendritic cell differentiation
Biological Process	GO:0032732	positive regulation of interleukin-1 production
Biological Process	GO:0032733	positive regulation of interleukin-10 production
Biological Process	GO:0032735	positive regulation of interleukin-12 production
Biological Process	GO:0032755	positive regulation of interleukin-6 production
Biological Process	GO:0032757	positive regulation of interleukin-8 production
Biological Process	GO:0032425	positive regulation of mismatch repair
Biological Process	GO:0090026	positive regulation of monocyte chemotaxis
Biological Process	GO:0034165	positive regulation of toll-like receptor 9 signaling pathway
Biological Process	GO:0045944	positive regulation of transcription by RNA polymerase II
Biological Process	GO:0032760	positive regulation of tumor necrosis factor production
Biological Process	GO:1905564	positive regulation of vascular endothelial cell proliferation
Biological Process	GO:0046598	positive regulation of viral entry into host cell
Biological Process	GO:0002840	regulation of T cell mediated immune response to tumor cell
Biological Process	GO:0032072	regulation of restriction endodeoxyribonuclease activity
Biological Process	GO:0002643	regulation of tolerance induction
Biological Process	GO:0006357	regulation of transcription by RNA polymerase II
Molecular Function	GO:0019958	C-X-C chemokine binding
Molecular Function	GO:0008301	DNA binding, bending
Molecular Function	GO:0070182	DNA polymerase binding
Molecular Function	GO:0140297	DNA-binding transcription factor binding
Molecular Function	GO:0050786	RAGE receptor binding
Molecular Function	GO:0003723	RNA binding
Molecular Function	GO:0061629	RNA polymerase II-specific DNA-binding transcription factor binding
Molecular Function	GO:0000405	bubble DNA binding
Molecular Function	GO:0042056	chemoattractant activity
Molecular Function	GO:0005125	cytokine activity
Molecular Function	GO:0003684	damaged DNA binding
Molecular Function	GO:0003690	double-stranded DNA binding
Molecular Function	GO:0000400	four-way junction DNA binding
Molecular Function	GO:0005178	integrin binding
Molecular Function	GO:0001530	lipopolysaccharide binding
Molecular Function	GO:0016829	lyase activity
Molecular Function	GO:0001786	phosphatidylserine binding
Molecular Function	GO:0048018	receptor ligand activity
Molecular Function	GO:0003697	single-stranded DNA binding
Molecular Function	GO:0097100	supercoiled DNA binding
Molecular Function	GO:0000976	transcription cis-regulatory region binding
Molecular Function	GO:0003713	transcription coactivator activity
Molecular Function	GO:0003714	transcription corepressor activity
Cellular Component	GO:0035868	alphav-beta3 integrin-HMGB1 complex
Cellular Component	GO:0009986	cell surface
Cellular Component	GO:0000793	condensed chromosome
Cellular Component	GO:0005783	endoplasmic reticulum
Cellular Component	GO:0005793	endoplasmic reticulum-Golgi intermediate compartment
Cellular Component	GO:0005768	endosome
Cellular Component	GO:0005576	extracellular region
Cellular Component	GO:0005615	extracellular space
Cellular Component	GO:1904813	ficolin-1-rich granule lumen
Cellular Component	GO:0005654	nucleoplasm
Cellular Component	GO:0005634	nucleus
Cellular Component	GO:0034774	secretory granule lumen
Cellular Component	GO:0017053	transcription repressor complex

InterPro / Pfam

InterPro	InterPro name
IPR009071	High mobility group box domain
IPR017967	HMG box A DNA-binding domain, conserved site
IPR036910	High mobility group box domain superfamily

Pfam	Pfam name
PF00505	HMG (high mobility group) box
PF09011	HMG-box domain

Reactome

Reactome	Reactome Name	Node type	Reactome Root	Reactome Root Name
R-HSA-1236974	ER-Phagosome pathway	Leaf	R-HSA-168256	Immune System
R-HSA-140342	Apoptosis induced DNA fragmentation	Leaf	R-HSA-5357801	Programmed Cell Death
R-HSA-166058	MyD88:MAL(TIRAP) cascade initiated on plasma membrane	Internal node	R-HSA-168256	Immune System
R-HSA-445989	TAK1-dependent IKK and NF-kappa-B activation	Internal node	R-HSA-168256	Immune System
R-HSA-5602498	MyD88 deficiency (TLR2/4)	Leaf	R-HSA-1643685	Disease
R-HSA-5603041	IRAK4 deficiency (TLR2/4)	Leaf	R-HSA-1643685	Disease
R-HSA-5620971	Pyroptosis	Leaf	R-HSA-5357801	Programmed Cell Death
R-HSA-5686938	Regulation of TLR by endogenous ligand	Leaf	R-HSA-168256	Immune System
R-HSA-6798695	Neutrophil degranulation	Leaf	R-HSA-168256	Immune System
R-HSA-879415	Advanced glycosylation endproduct receptor signaling	Leaf	R-HSA-168256	Immune System
R-HSA-933542	TRAF6 mediated NF-kB activation	Leaf	R-HSA-168256	Immune System

Subcellular location

Location	ECO term	Pubmed
Cell membrane	ECO:0000250	PubMed:11154118
Chromosome	ECO:0000250
Cytoplasm	ECO:0000269	PubMed:11154118
Cytoplasm	ECO:0000269	PubMed:12231511
Cytoplasm	ECO:0000269	PubMed:17114460
Cytoplasm	ECO:0000269	PubMed:20819940
Cytoplasm	ECO:0000269	PubMed:22869893
Cytoplasm	ECO:0000269	PubMed:29618516
Cytoplasm	ECO:0000269	PubMed:33147444
Cytoplasm	ECO:0000269	PubMed:34971702
Endoplasmic reticulum	ECO:0000269	PubMed:35239449
Endoplasmic reticulum-Golgi intermediate compartment	ECO:0000250
Endosome	ECO:0000250
Nucleus	ECO:0000269	PubMed:12231511
Nucleus	ECO:0000269	PubMed:17114460
Nucleus	ECO:0000269	PubMed:20819940
Nucleus	ECO:0000269	PubMed:22696656
Nucleus	ECO:0000269	PubMed:22869893
Nucleus	ECO:0000269	PubMed:27362237
Nucleus	ECO:0000269	PubMed:29618516
Nucleus	ECO:0000269	PubMed:33147444
Secreted	ECO:0000250	PubMed:12231511
Secreted	ECO:0000250	PubMed:14532127
Secreted	ECO:0000250	PubMed:15944249
Secreted	ECO:0000250	PubMed:19811284
Secreted	ECO:0000250	PubMed:22869893
Secreted	ECO:0000250	PubMed:33147444

Interactor | Variant | Drug

Phenotype

Tissue and cell type

Tissue	Cell type	Expression level	Reliability
adipose tissue	adipocytes	Medium	Supported
adrenal gland	glandular cells	Medium	Supported
appendix	endocrine cells	High	Supported
appendix	enterocytes	High	Supported
appendix	goblet cells	High	Supported
appendix	non-germinal center cells	High	Supported
bone marrow	hematopoietic cells	High	Supported
breast	adipocytes	Medium	Supported
breast	glandular cells	High	Supported
breast	myoepithelial cells	High	Supported
bronchus	respiratory epithelial cells	High	Supported
caudate	glial cells	High	Supported
cerebellum	Bergmann glia - nucleus	High	Supported
cerebellum	granular cells - nucleus	High	Supported
cerebellum	molecular layer cells - nucleus	High	Supported
cerebellum	white matter cells - nucleus	High	Supported
cerebral cortex	endothelial cells	Medium	Supported
cerebral cortex	glial cells	High	Supported
cerebral cortex	neuronal cells	Low	Supported
cervix	glandular cells	High	Supported
cervix	squamous epithelial cells	High	Supported
colon	endocrine cells	High	Supported
colon	endothelial cells	High	Supported
colon	enterocytes	High	Supported
colon	goblet cells	High	Supported
colon	mucosal lymphoid cells	High	Supported
duodenum	endocrine cells	High	Supported
duodenum	enterocytes	High	Supported
duodenum	goblet cells	High	Supported
duodenum	paneth cells	High	Supported
endometrium 1	cells in endometrial stroma	High	Supported
endometrium 1	glandular cells	High	Supported
endometrium 2	cells in endometrial stroma	High	Supported
endometrium 2	glandular cells	Medium	Supported
epididymis	glandular cells	High	Supported
esophagus	squamous epithelial cells	High	Supported
fallopian tube	glandular cells	High	Supported
gallbladder	glandular cells	High	Supported
heart muscle	cardiomyocytes	High	Supported
hippocampus	glial cells	High	Supported
hippocampus	neuronal cells	Low	Supported
kidney	cells in glomeruli	High	Supported
kidney	cells in tubules	High	Supported
liver	cholangiocytes	High	Supported
liver	hepatocytes	High	Supported
lung	alveolar cells	High	Supported
lung	macrophages	High	Supported
lymph node	germinal center cells	High	Supported
lymph node	non-germinal center cells	High	Supported
nasopharynx	respiratory epithelial cells	High	Supported
oral mucosa	squamous epithelial cells	High	Supported
ovary	ovarian stroma cells	High	Supported
pancreas	exocrine glandular cells	High	Supported
pancreas	pancreatic endocrine cells	Medium	Supported
parathyroid gland	glandular cells	Medium	Supported
placenta	decidual cells	High	Supported
placenta	trophoblastic cells	High	Supported
prostate	glandular cells	High	Supported
rectum	endocrine cells	High	Supported
rectum	endothelial cells	High	Supported
rectum	enterocytes	High	Supported
rectum	fibroblasts	High	Supported
rectum	goblet cells	High	Supported
rectum	mucosal lymphoid cells	High	Supported
rectum	peripheral nerve/ganglion	High	Supported
salivary gland	glandular cells	High	Supported
seminal vesicle	glandular cells	Low	Supported
skeletal muscle	myocytes	High	Supported
skin 1	cells in basal layer	High	Supported
skin 1	cells in granular layer	High	Supported
skin 1	cells in spinous layer	High	Supported
skin 1	eccrine glands	High	Supported
skin 1	endothelial cells	High	Supported
skin 1	fibrohistiocytic cells	High	Supported
skin 1	langerhans cells	High	Supported
skin 1	lymphocytes	High	Supported
skin 1	melanocytes	High	Supported
skin 1	vascular mural cells	High	Supported
skin 2	cells in basal layer	High	Supported
skin 2	cells in spinous layer	Medium	Supported
skin 2	endothelial cells	High	Supported
skin 2	fibrohistiocytic cells	High	Supported
skin 2	langerhans cells	Medium	Supported
skin 2	lymphocytes	High	Supported
skin 2	melanocytes	High	Supported
skin 2	vascular mural cells	High	Supported
small intestine	endocrine cells	High	Supported
small intestine	enterocytes	High	Supported
small intestine	goblet cells	High	Supported
small intestine	paneth cells	High	Supported
smooth muscle	smooth muscle cells	High	Supported
soft tissue 1	chondrocytes	Low	Supported
soft tissue 1	fibroblasts	High	Supported
soft tissue 1	peripheral nerve	High	Supported
soft tissue 2	fibroblasts	Medium	Supported
spleen	cells in red pulp	High	Supported
spleen	cells in white pulp	High	Supported
stomach 1	glandular cells	High	Supported
stomach 2	glandular cells	High	Supported
testis	Leydig cells	Medium	Supported
testis	pachytene spermatocytes	High	Supported
testis	peritubular cells	Medium	Supported
testis	round or early spermatids	High	Supported
testis	spermatogonia cells	High	Supported
thyroid gland	glandular cells	High	Supported
tonsil	germinal center cells	High	Supported
tonsil	non-germinal center cells	High	Supported
tonsil	squamous epithelial cells	High	Supported
urinary bladder	urothelial cells	High	Supported
vagina	squamous epithelial cells	High	Supported

Summary of P09429

Gene: HMGB1, HMG1
Protein: High mobility group protein B1

Structure

GO term

InterPro / Pfam

Reactome

Subcellular location

Interactor | Variant | Drug

Phenotype

Tissue and cell type

Disease

Summary of P09429

Gene: HMGB1, HMG1 Protein: High mobility group protein B1

Structure

GO term

InterPro / Pfam

Reactome

Subcellular location

Interactor | Variant | Drug

Phenotype

Tissue and cell type

Disease

Gene: HMGB1, HMG1
Protein: High mobility group protein B1